| Line | UNr12 | UNHmax12 | UNiD12 | UNd12 | UNSTP12 | Bra016271 | Bra038030 | Bra040132 | Bra017243 |
|---|---|---|---|---|---|---|---|---|---|
| RIL_1 | 0.0127 | 40.1 | 659.2 | 944.4 | 38.4 | 8.8 | 5.7 | 4.8 | 4.7 |
| RIL_103 | 0.0141 | 47.0 | 617.6 | 870.7 | 45.6 | 8.9 | 1.2 | 4.8 | -3.0 |
| RIL_115 | 0.0135 | 26.3 | 652.6 | 910.2 | 24.7 | 8.9 | 0.9 | -1.6 | -3.2 |
| RIL_12 | 0.0145 | 19.9 | 516.6 | 762.6 | 18.8 | 2.4 | -1.6 | 5.0 | -3.9 |
| RIL_124 | 0.0120 | 44.7 | 695.4 | 966.1 | 41.8 | 9.2 | 5.9 | -1.1 | 5.0 |
| RIL_131 | 0.0138 | 28.0 | 487.3 | 750.1 | 26.9 | 2.9 | 5.9 | 4.9 | -3.3 |
| RIL_136 | 0.0107 | 34.0 | 575.6 | 884.7 | 32.2 | 8.9 | 6.1 | -1.6 | 5.4 |
| RIL_143 | 0.0128 | 39.1 | 742.0 | 997.9 | 36.6 | 2.6 | 5.8 | -2.4 | 5.3 |
| RIL_146 | 0.0113 | 37.8 | 596.4 | 896.6 | 35.8 | 2.6 | 5.6 | -2.1 | 4.7 |
| RIL_147 | 0.0140 | 38.2 | 693.8 | 936.8 | 36.0 | 2.2 | -0.7 | -1.7 | 5.2 |
| UNr12 | UNHmax12 | UNiD12 | UNd12 | UNSTP12 | Bra016271 | Bra038030 | Bra040132 | Bra017243 | |
|---|---|---|---|---|---|---|---|---|---|
| UNr12 | 1.00 | -0.25 | -0.32 | -0.51 | -0.23 | -0.04 | -0.39 | 0.08 | -0.15 |
| UNHmax12 | -0.25 | 1.00 | 0.79 | 0.77 | 1.00 | 0.09 | 0.28 | 0.13 | -0.01 |
| UNiD12 | -0.32 | 0.79 | 1.00 | 0.97 | 0.78 | -0.03 | 0.30 | -0.09 | 0.20 |
| UNd12 | -0.51 | 0.77 | 0.97 | 1.00 | 0.75 | -0.03 | 0.36 | -0.10 | 0.21 |
| UNSTP12 | -0.23 | 1.00 | 0.78 | 0.75 | 1.00 | 0.09 | 0.27 | 0.14 | -0.02 |
| Bra016271 | -0.04 | 0.09 | -0.03 | -0.03 | 0.09 | 1.00 | -0.01 | -0.02 | -0.03 |
| Bra038030 | -0.39 | 0.28 | 0.30 | 0.36 | 0.27 | -0.01 | 1.00 | 0.03 | 0.04 |
| Bra040132 | 0.08 | 0.13 | -0.09 | -0.10 | 0.14 | -0.02 | 0.03 | 1.00 | -0.20 |
| Bra017243 | -0.15 | -0.01 | 0.20 | 0.21 | -0.02 | -0.03 | 0.04 | -0.20 | 1.00 |
| UNr12 | UNHmax12 | UNiD12 | UNd12 | UNSTP12 | Bra030612 | Bra010212 | Bra102212 | Bra101312 | Bra007112 | |
|---|---|---|---|---|---|---|---|---|---|---|
| UNr12 | 1 | 1694 | 768 | 22 | 2041 | 6291 | 9173 | 3227 | 2416 | 9701 |
| UNHmax12 | 1694 | 1 | 3 | 3 | 2 | 9702 | 6554 | 1623 | 8654 | 3079 |
| UNiD12 | 768 | 3 | 1 | 2 | 3 | 8770 | 8021 | 2076 | 7804 | 1536 |
| UNd12 | 22 | 3 | 2 | 1 | 4 | 9449 | 8108 | 1767 | 6085 | 2078 |
| UNSTP12 | 2041 | 2 | 3 | 4 | 1 | 9623 | 6041 | 1588 | 8241 | 3145 |
| Bra030612 | 6291 | 9702 | 8770 | 9449 | 9623 | 1 | 2194 | 7135 | 7878 | 9667 |
| Bra010212 | 9173 | 6554 | 8021 | 8108 | 6041 | 2194 | 1 | 4916 | 9702 | 8193 |
| Bra102212 | 3227 | 1623 | 2076 | 1767 | 1588 | 7135 | 4916 | 1 | 6312 | 4154 |
| Bra101312 | 2416 | 8654 | 7804 | 6085 | 8241 | 7878 | 9702 | 6312 | 1 | 5763 |
| Bra007112 | 9701 | 3079 | 1536 | 2078 | 3145 | 9667 | 8193 | 4154 | 5763 | 1 |
| threshold | 0.95 expectation | observed | |
|---|---|---|---|
| blup.mr.graph.UN.2012.10 | 10 | 0 | 1 |
| blup.mr.graph.UN.2012.20 | 20 | 1 | 13 |
| blup.mr.graph.UN.2012.30 | 30 | 4 | 28 |
| blup.mr.graph.UN.2012.50 | 50 | 12 | 57 |
So the networks are enriched for “real” connections
Do any of the the MR genes co-localize with QTL peaks for growth?
Yes!
| MR Cutoff | Network Genes | Network Genes under QTL | P-Value for enrichment |
|---|---|---|---|
| 10 | 1 | 0 | 1 |
| 20 | 13 | 9 | 6.9 E-13 |
| 30 | 28 | 9 | 5.0 E-09 |
| 50 | 57 | 21 | 9.9 E-21 |
Caveat: Linkage…
\[ growth \sim QTL\_marker\tag{1} \\ \\ VS \] \[ \\growth \sim QTL\_marker + gene\_expression\tag{2} \]
Do eQTL for the MR genes overlap with the growth QTL?
After reconstructing the network, calculate the Eigen gene for each module and then correlate with traits:
Blue: Cell division (pos correlation)
| module | term | ontology | FDR |
|---|---|---|---|
| blue | cell division | BP | 0.0000382 |
| blue | nucleosome assembly | BP | 0.0001382 |
| blue | microtubule-based movement | BP | 0.0010579 |
| blue | auxin metabolic process | BP | 0.0027352 |
| blue | regulation of meristem structural organization | BP | 0.0027352 |
| blue | leaf development | BP | 0.0035562 |
| blue | xylem and phloem pattern formation | BP | 0.0181424 |
| blue | microtubule nucleation | BP | 0.0188533 |
| blue | positive regulation of microtubule polymerization | BP | 0.0188533 |
| blue | regulation of cell cycle | BP | 0.0192759 |
| blue | DNA replication initiation | BP | 0.0229370 |
| blue | abaxial cell fate specification | BP | 0.0229370 |
| blue | fruit development | BP | 0.0229370 |
Cyan: Translation (pos correlation)
| module | term | ontology | FDR |
|---|---|---|---|
| cyan | translation | BP | 0.0000000 |
| cyan | cytosolic large ribosomal subunit | CC | 0.0000000 |
| cyan | nucleolus | CC | 0.0000000 |
| cyan | cytosolic small ribosomal subunit | CC | 0.0000000 |
| cyan | ribosome biogenesis | BP | 0.0000000 |
| cyan | vacuolar membrane | CC | 0.0000006 |
| cyan | mitochondrial respiratory chain complex I | CC | 0.0000310 |
| cyan | cell wall | CC | 0.0021796 |
| cyan | cytosolic ribosome | CC | 0.0046775 |
| cyan | chloroplast | CC | 0.0261363 |
| cyan | plasma membrane | CC | 0.0349344 |
MidnightBlue: Stress/defense? (pos correlation)
| module | term | ontology | FDR |
|---|---|---|---|
| midnightblue | vacuole | CC | 0.0000209 |
| midnightblue | toxin catabolic process | BP | 0.0000209 |
| midnightblue | response to wounding | BP | 0.0000499 |
| midnightblue | ER body | CC | 0.0000765 |
| midnightblue | sulfate assimilation | BP | 0.0000974 |
| midnightblue | glucosinolate biosynthetic process | BP | 0.0015902 |
| midnightblue | regulation of response to red or far red light | BP | 0.0042999 |
| midnightblue | chloroplast stroma | CC | 0.0044724 |
| midnightblue | male gamete generation | BP | 0.0044724 |
| midnightblue | response to cadmium ion | BP | 0.0081931 |
| midnightblue | post-embryonic root development | BP | 0.0081931 |
| midnightblue | glucosinolate catabolic process | BP | 0.0081931 |
| midnightblue | response to jasmonic acid | BP | 0.0098597 |
| midnightblue | response to herbivore | BP | 0.0102517 |
| midnightblue | regulation of glucosinolate biosynthetic process | BP | 0.0127414 |
| midnightblue | glutathione metabolic process | BP | 0.0214903 |
| midnightblue | cellular response to water deprivation | BP | 0.0236303 |
| midnightblue | heterotetrameric ADPG pyrophosphorylase complex | CC | 0.0260464 |
| midnightblue | stamen formation | BP | 0.0260464 |
| midnightblue | response to misfolded protein | BP | 0.0260464 |
| midnightblue | proteasome core complex assembly | BP | 0.0260464 |
| midnightblue | mitochondrial proton-transporting ATP synthase complex | CC | 0.0260464 |
| midnightblue | response to salt stress | BP | 0.0260464 |
| midnightblue | nitrile biosynthetic process | BP | 0.0260904 |
| midnightblue | oxidation-reduction process | BP | 0.0346123 |
| midnightblue | peroxisome | CC | 0.0346123 |
| midnightblue | defense response to bacterium | BP | 0.0346123 |
Brown: ? (neg correlation)
| module | term | ontology | FDR |
|---|---|---|---|
| brown | protein serine/threonine phosphatase complex | CC | 0.0005793 |
| brown | actin cytoskeleton organization | BP | 0.0005793 |
| brown | protein dephosphorylation | BP | 0.0019447 |
| brown | small GTPase mediated signal transduction | BP | 0.0495296 |
A10 (cyan, midnightblue, blue) and A03 (darkslateblue) overlap with growth QTL
Network analysis has defined possible mechanisms underlying growth trait QTL.
Linkage is a major caveat
Model comparison is encouraging that more than linkage is going on